Hello Jason,
I realized that I could also put this problem up on the github for pytraj,
https://github.com/Amber-MD/pytraj/issues/1605 , but I will also put the
two examples here since this is closer to pysander people (perhaps):
We can construct an options set for PB using gas_input as a starting point;
then use an example trajectory to execute pbsa:
> options = sander.gas_input(8)
> options.igb = 0
> options.ipb = 2
fn, tn = get_fn('ala3')
> traj = pt.Trajectory(fn, tn)
first=pt.esander(traj=traj, mm_options=options)
> second=pt.esander(traj=traj, mm_options=options)
Alternatively, you can just specify igb=10; which also works:
> fn, tn = get_fn('ala3')
> traj = pt.Trajectory(fn, tn)
> first=pt.esander(traj=traj, igb=10)
> second=pt.esander(traj=traj, igb=10)
These are both setup to use pytraj/pysander.
Hope this shines some light on it,
~David
Hi David,
> I don't think I've ever tried the PB interface through the sander API. Do
> you have an example script that shows the error you're seeing?
> Thanks,
> Jason
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Received on Sat Apr 02 2022 - 18:00:02 PDT
